Established populations of zebra mussels (Dreissena polymorpha) can promote blooms of Microcystis aeruginosa in oligotrophic systems. Since M. aeruginosa produces the hepatotoxin microcystin, blooms may have ecological implications. To assess the impact of toxin production by M. aeruginosa, Hexagenia spp. and lake sediment were collected at depths of 1.5, 3, 6, 10 meters, and from the deepest locations of Little Traverse Lake (LTL) and North Lake Leelanau (NLL) (Michigan) in May (prior to cyanobacterial blooms) and September (following cyanobacterial blooms) of 2004. Samples were analyzed for microcystin using enzyme linked immuno-sorbent assay (ELISA) and high performance liquid chromatography-mass spectrometry (HPLC-MS). Microcystin concentrations measured using ELISA and HPLC-MS were significantly correlated in Hexagenia spp. and lake sediments. Although microcystin does not bioaccumulate, spring values of Hexagenia spp. exceeded 1 μg/g (dw). Microcystin concentrations in Hexagenia spp. increased from spring to fall (LTL) and, in both lake basins, with increasing body length of Hexagenia spp. Fall sediment concentrations of microcystin increased with depth. These data suggest that in LTL and NLL, microcystin may be estimated in Hexagenia spp. and sediment using the ELISA method, and that Hexagenia spp. may be exposed to high values of microcystin in the absence of M. aeruginosa.